If you're smart enough to do a PhD, you're smart enough to figure out all of the scaling and operational bits. It's not rocket science. It's just operations.

Simply by asking relevant questions, practicing some things a bit, you'll get used to it.

And consider that it's different in every organization, and nobody does it really well frankly.

Given the pace of change, the varying technologies and flavour-of-the-month processes, it may always seem a little unwieldy an opaque: the feeling of 'not knowing everything' never goes away.

And I concur with the itronitron: read other people's code on the team, who are known to 'code well'.

It does not mean that algorithmically it's genius or even good - it just means that those are the styles/patterns that may be expected of you. It's like learning to say certain words a certain way. You'll get it soon and then forget you're doing it.

Don't fret you'll get all of this quickly.